from SAP.Bio.PDB import PDBParser if len(sys.argv) != 4: print("Expects three arguments,") print(" - FASTA alignment filename (expect two sequences)") print(" - PDB file one") print(" - PDB file two") sys.exit() # The alignment fa=AlignIO.read(open(sys.argv[1]), "fasta", generic_protein) pdb_file1=sys.argv[2] pdb_file2=sys.argv[3] # The structures p=PDBParser() s1=p.get_structure('1', pdb_file1) p=PDBParser() s2=p.get_structure('2', pdb_file2) # Get the models m1=s1[0] m2=s2[0] al=StructureAlignment(fa, m1, m2) # Print aligned pairs (r is None if gap) for (r1, r2) in al.get_iterator(): print("%s %s" % (r1, r2))
for i in range(0, L): residues[i].xtra["SS_PSEA"] = ss_seq[i] #os.system("rm "+fname) class PSEA(object): def __init__(self, model, filename): ss_seq = psea(filename) ss_seq = psea2HEC(ss_seq) annotate(model, ss_seq) self.ss_seq = ss_seq def get_seq(self): """ Return secondary structure string. """ return self.ss_seq if __name__ == "__main__": import sys from SAP.Bio.PDB import PDBParser # Parse PDB file p = PDBParser() s = p.get_structure('X', sys.argv[1]) # Annotate structure with PSEA sceondary structure info PSEA(s[0], sys.argv[1])
for residue in residue_list: if not is_aa(residue): continue rd=residue_depth(residue, surface) ca_rd=ca_depth(residue, surface) # Get the key res_id=residue.get_id() chain_id=residue.get_parent().get_id() depth_dict[(chain_id, res_id)]=(rd, ca_rd) depth_list.append((residue, (rd, ca_rd))) depth_keys.append((chain_id, res_id)) # Update xtra information residue.xtra['EXP_RD']=rd residue.xtra['EXP_RD_CA']=ca_rd AbstractPropertyMap.__init__(self, depth_dict, depth_keys, depth_list) if __name__=="__main__": import sys from SAP.Bio.PDB import PDBParser p=PDBParser() s=p.get_structure("X", sys.argv[1]) model=s[0] rd=ResidueDepth(model, sys.argv[1]) for item in rd: print(item)
from SAP.Bio.PDB import PDBParser if len(sys.argv) != 4: print("Expects three arguments,") print(" - FASTA alignment filename (expect two sequences)") print(" - PDB file one") print(" - PDB file two") sys.exit() # The alignment fa = AlignIO.read(open(sys.argv[1]), "fasta", generic_protein) pdb_file1 = sys.argv[2] pdb_file2 = sys.argv[3] # The structures p = PDBParser() s1 = p.get_structure('1', pdb_file1) p = PDBParser() s2 = p.get_structure('2', pdb_file2) # Get the models m1 = s1[0] m2 = s2[0] al = StructureAlignment(fa, m1, m2) # Print aligned pairs (r is None if gap) for (r1, r2) in al.get_iterator(): print("%s %s" % (r1, r2))
""" if self.rotran is None: raise PDBException("No transformation has been calculated yet") rot, tran=self.rotran rot=rot.astype('f') tran=tran.astype('f') for atom in atom_list: atom.transform(rot, tran) if __name__=="__main__": import sys from SAP.Bio.PDB import PDBParser, Selection p=PDBParser() s1=p.get_structure("FIXED", sys.argv[1]) fixed=Selection.unfold_entities(s1, "A") s2=p.get_structure("MOVING", sys.argv[1]) moving=Selection.unfold_entities(s2, "A") rot=numpy.identity(3).astype('f') tran=numpy.array((1.0, 2.0, 3.0), 'f') for atom in moving: atom.transform(rot, tran) sup=Superimposer() sup.set_atoms(fixed, moving)
for i in range(0, L): residues[i].xtra["SS_PSEA"]=ss_seq[i] #os.system("rm "+fname) class PSEA(object): def __init__(self, model, filename): ss_seq=psea(filename) ss_seq=psea2HEC(ss_seq) annotate(model, ss_seq) self.ss_seq=ss_seq def get_seq(self): """ Return secondary structure string. """ return self.ss_seq if __name__=="__main__": import sys from SAP.Bio.PDB import PDBParser # Parse PDB file p=PDBParser() s=p.get_structure('X', sys.argv[1]) # Annotate structure with PSEA sceondary structure info PSEA(s[0], sys.argv[1])
def PdbAtomIterator(handle): """Returns SeqRecord objects for each chain in a PDB file The sequences are derived from the 3D structure (ATOM records), not the SEQRES lines in the PDB file header. Unrecognised three letter amino acid codes (e.g. "CSD") from HETATM entries are converted to "X" in the sequence. In addition to information from the PDB header (which is the same for all records), the following chain specific information is placed in the annotation: record.annotations["residues"] = List of residue ID strings record.annotations["chain"] = Chain ID (typically A, B ,...) record.annotations["model"] = Model ID (typically zero) Where amino acids are missing from the structure, as indicated by residue numbering, the sequence is filled in with 'X' characters to match the size of the missing region, and None is included as the corresponding entry in the list record.annotations["residues"]. This function uses the Bio.PDB module to do most of the hard work. The annotation information could be improved but this extra parsing should be done in parse_pdb_header, not this module. """ # Only import PDB when needed, to avoid/delay NumPy dependency in SeqIO from SAP.Bio.PDB import PDBParser from SAP.Bio.SeqUtils import seq1 def restype(residue): """Return a residue's type as a one-letter code. Non-standard residues (e.g. CSD, ANP) are returned as 'X'. """ return seq1(residue.resname, custom_map=protein_letters_3to1) # Deduce the PDB ID from the PDB header # ENH: or filename? from SAP.Bio.File import UndoHandle undo_handle = UndoHandle(handle) firstline = undo_handle.peekline() if firstline.startswith("HEADER"): pdb_id = firstline[62:66] else: warnings.warn("First line is not a 'HEADER'; can't determine PDB ID") pdb_id = '????' struct = PDBParser().get_structure(pdb_id, undo_handle) model = struct[0] for chn_id, chain in sorted(model.child_dict.items()): # HETATM mod. res. policy: remove mod if in sequence, else discard residues = [ res for res in chain.get_unpacked_list() if seq1(res.get_resname().upper(), custom_map=protein_letters_3to1) != "X" ] if not residues: continue # Identify missing residues in the structure # (fill the sequence with 'X' residues in these regions) gaps = [] rnumbers = [r.id[1] for r in residues] for i, rnum in enumerate(rnumbers[:-1]): if rnumbers[i + 1] != rnum + 1: # It's a gap! gaps.append((i + 1, rnum, rnumbers[i + 1])) if gaps: res_out = [] prev_idx = 0 for i, pregap, postgap in gaps: if postgap > pregap: gapsize = postgap - pregap - 1 res_out.extend(restype(x) for x in residues[prev_idx:i]) prev_idx = i res_out.append('X' * gapsize) else: warnings.warn("Ignoring out-of-order residues after a gap", UserWarning) # Keep the normal part, drop the out-of-order segment # (presumably modified or hetatm residues, e.g. 3BEG) res_out.extend(restype(x) for x in residues[prev_idx:i]) break else: # Last segment res_out.extend(restype(x) for x in residues[prev_idx:]) else: # No gaps res_out = [restype(x) for x in residues] record_id = "%s:%s" % (pdb_id, chn_id) # ENH - model number in SeqRecord id if multiple models? # id = "Chain%s" % str(chain.id) # if len(structure) > 1 : # id = ("Model%s|" % str(model.id)) + id record = SeqRecord( Seq(''.join(res_out), generic_protein), id=record_id, description=record_id, ) # The PDB header was loaded as a dictionary, so let's reuse it all record.annotations = struct.header.copy() # Plus some chain specifics: record.annotations["model"] = model.id record.annotations["chain"] = chain.id # Start & end record.annotations["start"] = int(rnumbers[0]) record.annotations["end"] = int(rnumbers[-1]) # ENH - add letter annotations -- per-residue info, e.g. numbers yield record
""" if self.rotran is None: raise PDBException("No transformation has been calculated yet") rot, tran = self.rotran rot = rot.astype('f') tran = tran.astype('f') for atom in atom_list: atom.transform(rot, tran) if __name__ == "__main__": import sys from SAP.Bio.PDB import PDBParser, Selection p = PDBParser() s1 = p.get_structure("FIXED", sys.argv[1]) fixed = Selection.unfold_entities(s1, "A") s2 = p.get_structure("MOVING", sys.argv[1]) moving = Selection.unfold_entities(s2, "A") rot = numpy.identity(3).astype('f') tran = numpy.array((1.0, 2.0, 3.0), 'f') for atom in moving: atom.transform(rot, tran) sup = Superimposer() sup.set_atoms(fixed, moving)